SC Linux Workstations

Purpose

The Supercomputing Facility provides its users with access to several specially configured Linux workstations at two separate locations (see below) on campus. The primary function of such workstations is to provide stand-alone platforms for interactive pre- and post-processing tasks, including visualization, that are directly related to larger-scale computation on the supercomputers themselves. This manner of handling such tasks is more convenient and effective than the direct use of supercomputers for them.

Access requirements

We require the use of AMS to activate logins on the workstations.

To obtain access:

Locations and availability

Four Linux workstations (hostnames: sclab2.tamu.edu, sclab3.tamu.edu, sclab4.tamu.edu, sclab5.tamu.edu) have been installed in the Open Access Lab at Zachry in room 104 (ZACH 104). Additional information about the lab may be found here.

Three additional workstations (hostname: sclab1.tamu.edu,sclab6.tamu.edu,sclab7.tamu.edu) have also been installed at the Student Computing Center (SCC). This lab is typically open 24 hours during the weekdays and for a more limited time on the weekends.

Note: The SCLAB workstations were renamed from perkX.tamu.edu to sclabX.tamu.edu on September 18th, 2013. At present, each workstation is available at either name but users should switch to using sclabX.tamu.edu.

The daily schedule for both labs can be found here.

Obtaining help

The support staff at both labs mentioned above should be the initial point of contact for obvious hardware problems. All other issues (including hardware problems) should be reported to the Supercomputing Helpdesk by calling 845-0219 or by sending email to help@sc.tamu.edu. When sending email, be sure to follow these recommendations so we can help you in a prompt and efficient manner.

Usage policy and guidelines

The Linux workstation accounts are not to be used for work that is unrelated to the purpose for which a user was granted a supercomputing account.

These machines are meant primarily for interactive tasks (post-processing or visualization work). Users who need to work primarily through the batch systems on the supercomputers (submitting batch jobs and running programs on the command line) may do so using any of the windows machines in the open access labs. They simply need a secure shell window to log in to one or more of the supercomputers.

When both types of users wish to use the Linux workstations, those with non-interactive needs must yield use of the machines to those who have interactive/graphical/visualisation tasks to perform.

Furthermore, no user may occupy a workstation for more than 2 hours in a single sitting, unless there is no one else waiting to use a workstation.

Logging in

Users may login to these workstations either at the console (while sitting in front of the workstation), or remotely over the network using a secure shell connection (SSH). In either case, the user must supply a username and password to gain access to the account.

You must activate your username/password for the Linux workstations via AMS. The Linux workstations are represented by the SCLAB AMS resource.

Disk space management

There are several directories on each workstation where users may store files. It is important to understand the characteristics of each directory. Storing your data in the "wrong" place could mean that you will need to expend time and effort to find it again, and in certain cases, it may mean losing your data altogether!

Directory Name Space Backed up? 1 Persistent? 2 Shared 3 Over
Network?
/home/user 140 MB No Yes No
/scratch/user 16 GB max No No No
  1. Backed up data is that which is written to tape so that it may be recovered in the event the copy on disk storage is corrupted/destroyed. None of the directories listed above are backed up to tape.
  2. Persistent storage means that data will not be deleted across system re-boots, or by automated administrative scripts. In some systems, certain directories such as /tmp can be "cleaned out" automatically by the OS when the system comes back up after a re-boot. Data in such "temporary" directories may also be deleted by administrative scripts which try to ensure sufficient empty space by periodically deleting older files in these shared disk areas. The /scratch filesystem on each workstation is automatically cleaned up by an automated script whenever it fills up to 80% capacity. The script keeps deleting files (oldest first) until the filesystem is only 20% full.
  3. Directories which are not shared, like /scratch/aggie or /home/aggie for instance, represent separate and independent disk storage that is local to each workstation. Saving a file in /scratch/aggie on the workstation sclab2.tamu.edu means that you cannot access it in /scratch/aggie on any workstation other than sclab2.tamu.edu. You might find that even when you later return to sclab2.tamu.edu to access the file, it may have been deleted by the automated cleanup script (see note 2). You have been warned!

Locally installed software

The following software packages have been installed on each of the Linux workstations to enable users to offload postprocessing and visualization tasks from the heavily loaded (and therefore interactively less responsive) supercomputers.

In the course of maintaining these packages on the workstations, whenever we become aware of problems/issues with any package, we will post solutions/work-arounds to the problems in the section below.

The following commericial (licensed) applications are presently installed.
SoftwareCommand
Abaqus 6.12 CAEabq6121 cae (1)
Matlab 2013amatlab
  1. NOTE: for users that are running Abaqus CAE and Viewer on a SCLAB workstation and using X11 forwarding to display the GUI on their Windows PC. The -mesa command line option should be used if your X11 emulator does not support OpenGL (eg. Xming).
In addition to commercial applications, there is a plethora of open-source software installed on these systems. These include:
SoftwareCommand
Gracexmgrace
GROMACS(see: rpm -ql gromacs | grep bin)
LAMMPSlmp_g++
LibreOfficeooffice
NAMDnamd
Ncviewncview
OpenFOAM(see: rpm -ql OpenFOAM | grep /bin/)
Paraviewparaview
RStudiorstudio
TexLivelatex, dvips, bibtex, etc.

and many more. For a complete listing of installed software, see this page (sclab0.tamu.edu as of 26sep2013).

Launching remote software

If there is a need to launch software that resides on one of the supercomputers but have it display it's graphical interface on the Linux workstation where the user is sitting, the following instructions can be used:

Assume the program name is "xemacs" and that it resides on and will be executed on the machine "eos". At the prompt in a unix shell window (on your workstation), type:

ssh -X eos

Enter your (eos) password in response to the password prompt generated by the ssh program. Once you are logged in to eos, type:

xemacs

Hardware

ComponentSpecification
SystemDell Optiplex 960
CPUIntel Core2 Duo E8500, 3.16Ghz
Architecturex86_64
Operating SystemFedora 19 64Bit
Kernel Version3.10.10-200.fc19.x86_64 (as of 12sep2013)
Main Memory4GB
Hard Disk250GB
Network100Mbps Ethernet

For a detailed listing of the types of hardware provided, see this page (sclab0.tamu.edu as of 18sep2013)